Hi Willem, I had created an R-Package containing the CEL files from those two studies. You can retrieve it from our local repository. Within R call repUrl <- contrib.url("http://www.ebi.ac.uk/huber-srv/data/Rrepos") install.packages("ALLcelfiles", contriburl=repUrl) Let me know if you encounter any problems with this. The vignette of the package is quite basic, but at least mentions how to compare the raw AffyBatch object with the preprocessed ExpressionSet in the ALL package. In the long run, I guess this package should rather be added to the Bioconductor experiment data section, but with the new release coming up, maybe now is not the best time for that. Best regards, Joern Talloen, Willem [PRDBE] wrote: > Hi, > > I would like to do some probe-level analysis on a widely used Affymetrix data set. > The most logical choice is the ALL data set (Chiaretti et al 2004, 2005), but I cannot find the CEL files on Arrayexpress or GEO. > > Can anybody help me with this? > > Thanks in advance, > Willem > > [[From a mail from 2007-11-02 16:56:42 GMT on the BioC list; > >> Note that the package ALL only contains the RMA-preprocessed data. There may be a second data package containing the >raw CEL files of this data set soon. ]] >> -- Joern Toedling EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Phone +44(0)1223 492566 Email toedling at ebi.ac.uk